We have talked about how joint restrictions can limit ankle dorsiflexion and subsequently, the ability to deep squat properly.
Your calf muscle could also be limiting this range of motion. The soleus and gastrocnemius (gastroc) make up the calf or lower leg. Each of these muscles has a different point of origin and therefore needs to be stretched differently. The gastroc originates above the knee (making it a knee flexor), so it is stretched when the knee is in extension, or straight, and the ankle is dorsiflexed.Most people do a good job of stretching the lower leg this way; however the deeper soleus is often neglected.
The soleus does not cross the knee joint, so it can only be stretched by putting the gastroc on slack, which is achieved by flexing the knee joint (or more simply, bending your knee) and then dorsiflexing at the ankle. Since, a squat requires ankle dorsiflexion while your knee is bent; the soleus is the primary muscle that restricts that movement.